From: Francesco Pietra (
Date: Sun Jul 05 2020 - 10:38:46 CDT

running psfgen from vmd in text mode, I would like that the spatial
arrangement of an organic molecule surrounded by smaller molecule is
conserved. Although there are no clashes among the pdd in /parts, psfgen
displaces the bigger molecule out of the assembly of smaller molecules.

Is any way to conserve, more or less, the initial spatial arrangement?

thanks for advice
francesco pietra